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        Note that additional data was saved in multiqc_data when this report was generated.

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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.21

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/pacvar analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2024-11-08, 20:54 UTC based on data in: /Users/tanyajain/Desktop/nextflow_fun/pacvar/work/85/bc9c235551d9d08c38a3b25c39ee91

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        WorkflowNextflow24.4.4
        nf-core/pacvar1.0.dev0

        nf-core/pacvar Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.

        Methods

        Data was processed using nf-core/pacvar v1.0dev of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

        The pipeline was executed with Nextflow v24.04.4 (Di Tommaso et al., 2017) with the following command:

        nextflow run main.nf --outdir out2 -profile docker,test -resume

        References

        • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
        • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
        • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
        • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
        Notes:
        • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
        • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
        • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

        nf-core/pacvar Workflow Summary

        - this information is collected when the pipeline is started.

        Core Nextflow options

        runName
        condescending_mcclintock
        containerEngine
        docker
        launchDir
        /Users/tanyajain/Desktop/nextflow_fun/pacvar
        workDir
        /Users/tanyajain/Desktop/nextflow_fun/pacvar/work
        projectDir
        /Users/tanyajain/Desktop/nextflow_fun/pacvar
        userName
        tanyajain
        profile
        docker,test
        configFiles
        N/A

        Input/output options

        input
        https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/pacvar/pacbio_data/samplesheet_longread_puretarget.csv
        outdir
        out2
        barcodes
        https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/pacvar/pacbio_data/barcodes_D01.fasta

        Reference genome options

        genome
        GATK.GRCh38
        fasta
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta

        Institutional config options

        config_profile_name
        Test profile
        config_profile_description
        Minimal test dataset to check pipeline function

        Other parameters

        workflow
        repeat
        intervals
        https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/pacvar/pacbio_data/intervals.bed
        fasta_fai
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
        dbsnp
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
        dbsnp_tbi
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi
        dict
        s3://ngi-igenomes/igenomes//Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict

        MultiQC v1.21 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.